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This article presents a real time Unmanned Aerial Vehicles UAVs 3D pose estimation method using planar object tracking, in order to be used on the control system of a UAV. The method explodes the rich information obtained by a projective transformation of planar objects on a calibrated camera. The algorithm obtains the metric and projective components of a reference object (landmark or helipad) with respect to the UAV camera coordinate system, using a robust real time object tracking based on homographies. The algorithm is validated on real flights that compare the estimated data against that obtained by the inertial measurement unit IMU, showing that the proposed method robustly estimates the helicopter's 3D position with respect to a reference landmark, with a high quality on the position and orientation estimation when the aircraft is flying at low altitudes, a situation in which the GPS information is often inaccurate. The obtained results indicate that the proposed algorithm is suitable for complex control tasks, such as autonomous landing, accurate low altitude positioning and dropping of payloads.